6T90: OCT4-SOX2-bound nucleosome - SHL-6
OCT4-SOX2-bound nucleosome - SHL-6. Determined by electron microscopy at 3.05 Å resolution. Released 6 May 2020.
- Method
- Electron microscopy
- Resolution
- 3.05 Å
- Organisms
- Homo sapiens, synthetic construct, Aequorea victoria
- Chains
- 12
- Atoms
- 13,031
- Mol. weight
- 288.37 kDa
- Ligands
- PTD
- Released
- 6 May 2020
Explore 6T90 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6T90 contains 47 α-helices and 20 β-strands across 10 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chains A and E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 42-43 | 2 | |
| α-helix | 46-57 | 12 | |
| α-helix | 65-79 | 15 | |
| β-strand | 84-85 | 2 | 1 |
| α-helix | 87-114 | 28 | |
| β-strand | 119-120 | 2 | 2 |
| α-helix | 122-132 | 11 | |
Chains B and F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-29 | 4 | |
| α-helix | 32-41 | 10 | |
| β-strand | 46-47 | 2 | 2 |
| α-helix | 51-76 | 26 | |
| β-strand | 81-82 | 2 | 1 |
| α-helix | 84-92 | 9 | |
| β-strand | 98-99 | 2 | 3 |
Chain C: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-21 | 4 | |
| α-helix | 29-37 | 9 | |
| β-strand | 43-44 | 2 | 4 |
| α-helix | 47-73 | 27 | |
| β-strand | 78-79 | 2 | 5 |
| α-helix | 81-89 | 9 | |
| α-helix | 92-97 | 6 | |
| α-helix | 101 | 1 | |
| β-strand | 102-103 | 2 | 6 |
| α-helix | 114-116 | 3 | |
Chains D and H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 39-49 | 11 | |
| β-strand | 54-55 | 2 | 5 |
| α-helix | 57-84 | 28 | |
| β-strand | 89-90 | 2 | 4 |
| α-helix | 92-102 | 11 | |
| α-helix | 105-123 | 19 | |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-21 | 4 | |
| α-helix | 29-36 | 8 | |
| β-strand | 43-44 | 2 | 9 |
| α-helix | 48-73 | 26 | |
| β-strand | 78-79 | 2 | 10 |
| α-helix | 81-89 | 9 | |
| α-helix | 92-97 | 6 | |
| β-strand | 102-103 | 2 | 3 |
| α-helix | 114-116 | 3 | |
Chain K: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 139-159 | 21 | |
| α-helix | 164-175 | 12 | |
| α-helix | 181-188 | 8 | |
| α-helix | 194-209 | 16 | |
Chain L: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 42-45 | 4 | |
| α-helix | 47-62 | 16 | |
| α-helix | 68-80 | 13 | |
| α-helix | 84-104 | 21 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3.1 | A | protein | 139 | Homo sapiens | P68431 (AlphaFold model) |
| Histone H4 | B, F | protein | 106 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 1-B/E | C, G | protein | 133 | Homo sapiens | P04908 (AlphaFold model) |
| Histone H2B type 1-J | D, H | protein | 128 | Homo sapiens | P06899 (AlphaFold model) |
| Histone H3.1 | E | protein | 137 | Homo sapiens | P68431 (AlphaFold model) |
| DNA (146-mer) | I | DNA | 153 | synthetic construct | |
| DNA (146-mer) | J | DNA | 147 | synthetic construct | |
| Green fluorescent protein,POU domain, class 5, transcription factor 1 | K | protein | 643 | Aequorea victoria, Homo sapiens | P42212, Q01860 |
| Transcription factor SOX-2 | L | protein | 105 | Homo sapiens | P48431 |
Sequence of entity 1 (A), FASTA
>6T90_1 Histone H3.1 (chains A)
GSHMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQK
STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKR
VTIMPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>6T90_2 Histone H4 (chains B, F)
GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRG
VLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>6T90_3 Histone H2A type 1-B/E (chains C, G)
GSHMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLE
YLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLL
PKKTESHHKAKGK
Sequence of entity 4 (D, H), FASTA
>6T90_4 Histone H2B type 1-J (chains D, H)
GSHMPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISS
KAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTK
AVTKYTSA
Sequence of entity 5 (E), FASTA
>6T90_5 Histone H3.1 (chains E)
GSHMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQK
STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKR
VTIMPKDIQLARRIRGE
Sequence of entity 6 (I), FASTA
>6T90_6 DNA (146-MER) (chains I)
ATCCTGGAGACTTTGTTATGCAAATCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCT
TAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCT
CCAGGCACGTGTCAGATATATACATCCTGTGAT
Sequence of entity 7 (J), FASTA
>6T90_7 DNA (146-MER) (chains J)
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGATTTGCATAACAAAGTCTCCAG
Sequence of entity 8 (K), FASTA
>6T90_8 Green fluorescent protein,POU domain, class 5, transcription factor 1 (chains K)
MDWSHPQFEKSAVDENLYFQGGMVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDA
TYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERT
IFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQ
KNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEKRDH
MVLLEFVTAAGITLGMDELYKEAAAKEAAAKMAGHLASDFAFSPPPGGGGDGPGGPEPGW
VDPRTWLSFQGPPGGPGIGPGVGPGSEVWGIPPCPPPYEFCGGMAYCGPQVGVGLVPQGG
LETSQPEGEAGVGVESNSDGASPEPCTVTPGAVKLEKEKLEQNPEESQDIKALQKELEQF
AKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICRFEALQLSFKNMCKLRPLLQKWVE
EADNNENLQEICKAETLVQARKRKRTSIENRVRGNLENLFLQCPKPTLQQISHIAQQLGL
EKDVVRVWFCNRRQKGKRSSSDYAQREDFEAAGSPFSGGPVSFPLAPGPHFGTPGYGSPH
FTALYSSVPFPEGEAFPPVSVTTLGSPMHSNLPETGGHHHHHH
Sequence of entity 9 (L), FASTA
>6T90_9 Transcription factor SOX-2 (chains L)
MDWSHPQFEKSAVDENLYFQGGMSPDRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISK
RLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKT
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| PTD | Pentanedial | C5 H8 O2 | 9 |
Primary citation
Mechanisms of OCT4-SOX2 motif readout on nucleosomes. Michael, A.K., Grand, R.S., Isbel, L. et al. Science (2020) 368:1460-1465. DOI 10.1126/science.abb0074 · PubMed
Other PDB entries of the same protein (UniProt P68431 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5SVY 1.05 Å, MORC3 CW in complex with histone H3K4me1
- 2V89 1.1 Å, Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution
- 5SZC 1.19 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
- 5SZB 1.2 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
- 6BHD 1.25 Å, Crystal structure of SETDB1 with a modified H3 peptide
- 4UP0 1.28 Å, Ternary crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and…
- 5WXH 1.3 Å, Crystal structure of TAF3 PHD finger bound to H3K4me3
- 5FFV 1.3 Å, Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone…
- 4L7X 1.35 Å, Crystal structure of the DIDO PHD finger in complex with H3K4me3
- 6BHE 1.35 Å, Crystal structure of SETDB1 with a modified H3 peptide
- 6BHI 1.4 Å, Crystal structure of SETDB1 with a modified H3 peptide
- 3ASL 1.41 Å, Structure of UHRF1 in complex with histone tail
Browse structure collections
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